Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    description Rank Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1382 to 1431 of 3228 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] 674 HIF3A 226.497 214.355 1.05664
    i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] 1162 NKIRAS2 220.758 215.097 1.02632
    immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] 1888 ICT1 218.414 216.131 1.01056
    immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] 1706 IGBP1 223.846 220.847 1.01358
    imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 926 IMMP2L 217.942 210.139 1.03713
    importin 4. [refseq;acc:nm_024658] 2356 no value 220.921 221.863 1.00426
    importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 2709 220.521 220.395 1.00057
    importin 8; ran-binding protein 8. [refseq;acc:nm_006390] 2710 IPO8
    importin 9. [refseq;acc:nm_018085] 2860 no value 0.00001 0.00001 1
    importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] 1952 KPNA1 211.647 213.724 1.00981
    importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 2780 KPNA2 0.00001 0.00001 1
    importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 1018 KPNA3 217.361 210.554 1.03233
    importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 1016 KPNA4 217.369 210.561
    importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131] 1970 KPNA6 211.62 213.683 1.00975
    importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] 2523 KPNB1 201.96 201.488 1.00234
    importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] 1676 TNPO1 218.691 215.645 1.01413
    importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] 1474 RANBP5 218.582 214.427 1.01938
    importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 1459 CSE1L 192.336 188.637 1.01961
    indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] 2225 INMT 221.509 220.108 1.00637
    inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370] 806 GPR84 212.386 221.785 1.04425
    inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 500 ING2 224.662 240.673 1.07127
    inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] 506 ING1 224.535 240.476 1.071
    inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] 1154 PPA1 224.307 230.242 1.02646
    inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] 1155 PPA2
    inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] 1695 IMPDH1 218.937 215.971 1.01373
    inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 1693 IMPDH2
    inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968] 1433 OCRL 220.987 225.468 1.02028
    inositol polyphosphate multikinase. [refseq;acc:nm_152230] 1724 IPMK 217.676 220.53 1.01311
    inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] 544 INPP4A 222.156 208.201 1.06703
    inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] 542 INPP4B
    inositol polyphosphate-5-phosphatase; phosphatidylinositol polyphosphate 5-phosphatase type iv; phosphatidylinositol (4,5) bisphosphate 5-phosphatase. [refseq;acc:nm_019892] 2912 INPP5E 0.00001 0.00001 1
    inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] 1727 IMPA1 210.366 213.118 1.01308
    inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] 1728 IMPA2 210.358 213.103 1.01305
    insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663] 2106 ISL1 197.489 196.061 1.00728
    insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] 2200 ISL2 196.748 195.466 1.00656
    integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] 2244 ITM2A 209.197 207.915 1.00617
    integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] 2242 ITM2B
    integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] 2243 ITM2C
    integral membrane protein cii-3b. [sptrembl;acc:o75609] 1206 no value 207.646 212.891 1.02526
    integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006] 3224 ITGA3 0.00001 0.00001 1
    integrin alpha-6 precursor (vla-6) (cd49f). [swissprot;acc:p23229] 3158 ITGA6
    integrin alpha-7 precursor. [swissprot;acc:q13683] 2978 ITGA7
    integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556] 2905 ITGB1
    integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [swissprot;acc:p05107] 2873 ITGB2
    integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] 3195 ITGB3
    integrin beta-7 precursor. [swissprot;acc:p26010] 2951 ITGB7
    integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] 1251 ILK 219.354 224.7 1.02437
    interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894] 2600 HYAL3 224.877 225.193 1.00141
    interleukin enhancer binding factor 2; nuclear factor of activated t-cells, 45-kda. [refseq;acc:nm_004515] 2930 ILF2 0.00001 0.00001 1
    interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] 1108 FOXK2 218.006 212.119 1.02775

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/